Multiple sequence alignment - TraesCS4D01G170400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G170400 chr4D 100.000 3660 0 0 1 3660 296724474 296728133 0.000000e+00 6759.0
1 TraesCS4D01G170400 chr4D 86.058 416 36 14 467 872 464169521 464169924 9.390000e-116 427.0
2 TraesCS4D01G170400 chr4A 90.362 1463 47 27 1371 2811 192629022 192627632 0.000000e+00 1834.0
3 TraesCS4D01G170400 chr4A 88.627 466 22 9 883 1348 192629448 192629014 4.160000e-149 538.0
4 TraesCS4D01G170400 chr4A 95.208 313 6 4 2798 3107 192627614 192627308 1.530000e-133 486.0
5 TraesCS4D01G170400 chr4A 88.525 427 14 12 3267 3660 192626983 192626559 5.500000e-133 484.0
6 TraesCS4D01G170400 chr4A 89.796 98 2 5 1611 1704 734094309 734094402 6.420000e-23 119.0
7 TraesCS4D01G170400 chr4A 100.000 41 0 0 3169 3209 192627293 192627253 3.920000e-10 76.8
8 TraesCS4D01G170400 chr5D 98.066 879 16 1 1 879 41884265 41885142 0.000000e+00 1528.0
9 TraesCS4D01G170400 chr5D 97.241 870 19 5 1 866 546675476 546676344 0.000000e+00 1469.0
10 TraesCS4D01G170400 chr2D 94.344 884 45 4 1 880 373764468 373765350 0.000000e+00 1351.0
11 TraesCS4D01G170400 chr1D 92.963 881 56 5 3 879 397642187 397641309 0.000000e+00 1279.0
12 TraesCS4D01G170400 chr4B 86.375 1233 52 43 2459 3626 366927107 366928288 0.000000e+00 1240.0
13 TraesCS4D01G170400 chr4B 93.683 744 19 8 1681 2409 366926366 366927096 0.000000e+00 1088.0
14 TraesCS4D01G170400 chr4B 92.068 769 24 9 880 1642 366925628 366926365 0.000000e+00 1048.0
15 TraesCS4D01G170400 chr2B 91.603 786 47 12 1 781 658936187 658936958 0.000000e+00 1068.0
16 TraesCS4D01G170400 chr2B 96.875 32 1 0 2103 2134 52655439 52655408 2.000000e-03 54.7
17 TraesCS4D01G170400 chr1A 88.862 826 64 10 60 880 347349449 347348647 0.000000e+00 990.0
18 TraesCS4D01G170400 chr1A 93.103 87 1 4 1611 1697 507081841 507081760 4.960000e-24 122.0
19 TraesCS4D01G170400 chr1A 89.691 97 2 3 1611 1707 320485589 320485677 2.310000e-22 117.0
20 TraesCS4D01G170400 chr2A 87.302 882 59 25 2 882 739899602 739898773 0.000000e+00 959.0
21 TraesCS4D01G170400 chrUn 85.860 884 85 24 1 851 19786331 19785455 0.000000e+00 904.0
22 TraesCS4D01G170400 chrUn 89.189 481 43 5 1 475 92964293 92963816 3.150000e-165 592.0
23 TraesCS4D01G170400 chr7A 90.211 521 44 7 1 519 69491359 69491874 0.000000e+00 673.0
24 TraesCS4D01G170400 chr7D 90.052 382 30 5 507 882 631440253 631440632 4.250000e-134 488.0
25 TraesCS4D01G170400 chr7D 88.350 103 4 6 1601 1703 518683816 518683910 2.310000e-22 117.0
26 TraesCS4D01G170400 chr7D 94.444 36 1 1 2104 2139 554334112 554334078 2.000000e-03 54.7
27 TraesCS4D01G170400 chr3B 91.489 94 3 4 1610 1703 771737662 771737750 1.380000e-24 124.0
28 TraesCS4D01G170400 chr6D 90.625 96 1 3 1608 1703 427344942 427344855 1.790000e-23 121.0
29 TraesCS4D01G170400 chr6D 87.619 105 5 2 1607 1711 403969119 403969215 8.310000e-22 115.0
30 TraesCS4D01G170400 chr6B 90.625 96 1 2 1608 1703 13827613 13827526 1.790000e-23 121.0
31 TraesCS4D01G170400 chr7B 96.875 32 1 0 2104 2135 600566670 600566701 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G170400 chr4D 296724474 296728133 3659 False 6759.000000 6759 100.000000 1 3660 1 chr4D.!!$F1 3659
1 TraesCS4D01G170400 chr4A 192626559 192629448 2889 True 683.760000 1834 92.544400 883 3660 5 chr4A.!!$R1 2777
2 TraesCS4D01G170400 chr5D 41884265 41885142 877 False 1528.000000 1528 98.066000 1 879 1 chr5D.!!$F1 878
3 TraesCS4D01G170400 chr5D 546675476 546676344 868 False 1469.000000 1469 97.241000 1 866 1 chr5D.!!$F2 865
4 TraesCS4D01G170400 chr2D 373764468 373765350 882 False 1351.000000 1351 94.344000 1 880 1 chr2D.!!$F1 879
5 TraesCS4D01G170400 chr1D 397641309 397642187 878 True 1279.000000 1279 92.963000 3 879 1 chr1D.!!$R1 876
6 TraesCS4D01G170400 chr4B 366925628 366928288 2660 False 1125.333333 1240 90.708667 880 3626 3 chr4B.!!$F1 2746
7 TraesCS4D01G170400 chr2B 658936187 658936958 771 False 1068.000000 1068 91.603000 1 781 1 chr2B.!!$F1 780
8 TraesCS4D01G170400 chr1A 347348647 347349449 802 True 990.000000 990 88.862000 60 880 1 chr1A.!!$R1 820
9 TraesCS4D01G170400 chr2A 739898773 739899602 829 True 959.000000 959 87.302000 2 882 1 chr2A.!!$R1 880
10 TraesCS4D01G170400 chrUn 19785455 19786331 876 True 904.000000 904 85.860000 1 851 1 chrUn.!!$R1 850
11 TraesCS4D01G170400 chr7A 69491359 69491874 515 False 673.000000 673 90.211000 1 519 1 chr7A.!!$F1 518

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
663 738 0.032615 AAAAGCCACACCACCCTCAA 60.033 50.000 0.0 0.0 0.00 3.02 F
1008 1086 0.801251 CCAGCTTTCTCGCCTTTCTG 59.199 55.000 0.0 0.0 0.00 3.02 F
2296 2407 2.433838 CTGCTCCTCACACAGCGG 60.434 66.667 0.0 0.0 38.59 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2565 0.316204 ACACGGAAGGAACACGGTAG 59.684 55.0 0.00 0.00 0.00 3.18 R
2449 2566 0.752054 AACACGGAAGGAACACGGTA 59.248 50.0 0.00 0.00 0.00 4.02 R
3292 3746 0.179018 CAGCTGGGCCTGGTAATACC 60.179 60.0 15.02 1.71 39.22 2.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 372 0.250684 ATTGTGTGTGGCCGATGTGA 60.251 50.000 0.00 0.00 0.00 3.58
663 738 0.032615 AAAAGCCACACCACCCTCAA 60.033 50.000 0.00 0.00 0.00 3.02
857 935 7.509546 ACTGAGACTTCCTTAAAAATCAGTCA 58.490 34.615 0.00 0.00 41.60 3.41
916 994 6.987992 ACACAAGTAATTTGAGACGGAAGTAA 59.012 34.615 0.00 0.00 41.63 2.24
917 995 7.660208 ACACAAGTAATTTGAGACGGAAGTAAT 59.340 33.333 0.00 0.00 41.63 1.89
918 996 9.146984 CACAAGTAATTTGAGACGGAAGTAATA 57.853 33.333 0.00 0.00 41.63 0.98
960 1038 2.603473 TGAGTGACCACCGGGGAG 60.603 66.667 4.41 0.00 41.15 4.30
1008 1086 0.801251 CCAGCTTTCTCGCCTTTCTG 59.199 55.000 0.00 0.00 0.00 3.02
1226 1306 4.404640 CATGCTGTAATTGATCCATCCCT 58.595 43.478 0.00 0.00 0.00 4.20
1347 1427 3.755905 GCCTGCTAGCTCTTTCTTTCTTT 59.244 43.478 17.23 0.00 0.00 2.52
1679 1768 7.918643 AGTAGTAGTGATCTAAACGCTCTTAC 58.081 38.462 0.00 0.00 0.00 2.34
1781 1871 6.659242 GGAGATTTGGATTGAAACAGTAGGAA 59.341 38.462 0.00 0.00 0.00 3.36
1811 1906 7.728532 ACACATACATATGTAGATGTAGGACCA 59.271 37.037 23.57 1.79 43.50 4.02
2199 2306 6.036517 GCTACTGTATATGCAAGCCATATGAC 59.963 42.308 3.65 0.00 44.74 3.06
2296 2407 2.433838 CTGCTCCTCACACAGCGG 60.434 66.667 0.00 0.00 38.59 5.52
2297 2408 4.687215 TGCTCCTCACACAGCGGC 62.687 66.667 0.00 0.00 38.59 6.53
2415 2532 6.998074 TGGTCTATTGATTCTCTCTCTCTCTC 59.002 42.308 0.00 0.00 0.00 3.20
2417 2534 7.389053 GGTCTATTGATTCTCTCTCTCTCTCTC 59.611 44.444 0.00 0.00 0.00 3.20
2419 2536 8.370940 TCTATTGATTCTCTCTCTCTCTCTCTC 58.629 40.741 0.00 0.00 0.00 3.20
2421 2538 6.166984 TGATTCTCTCTCTCTCTCTCTCTC 57.833 45.833 0.00 0.00 0.00 3.20
2424 2541 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2425 2542 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2426 2543 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2427 2544 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2428 2545 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2429 2546 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2430 2547 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2431 2548 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2432 2549 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2433 2550 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2434 2551 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2435 2552 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2436 2553 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2437 2554 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2438 2555 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
2439 2556 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
2440 2557 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
2441 2558 4.964897 TCTCTCTCTCTCTCTCTCTCACAT 59.035 45.833 0.00 0.00 0.00 3.21
2442 2559 6.136155 TCTCTCTCTCTCTCTCTCTCACATA 58.864 44.000 0.00 0.00 0.00 2.29
2443 2560 6.784473 TCTCTCTCTCTCTCTCTCTCACATAT 59.216 42.308 0.00 0.00 0.00 1.78
2444 2561 6.997655 TCTCTCTCTCTCTCTCTCACATATC 58.002 44.000 0.00 0.00 0.00 1.63
2445 2562 6.784473 TCTCTCTCTCTCTCTCTCACATATCT 59.216 42.308 0.00 0.00 0.00 1.98
2446 2563 6.997655 TCTCTCTCTCTCTCTCACATATCTC 58.002 44.000 0.00 0.00 0.00 2.75
2447 2564 6.014242 TCTCTCTCTCTCTCTCACATATCTCC 60.014 46.154 0.00 0.00 0.00 3.71
2448 2565 5.013079 TCTCTCTCTCTCTCACATATCTCCC 59.987 48.000 0.00 0.00 0.00 4.30
2449 2566 4.913355 TCTCTCTCTCTCACATATCTCCCT 59.087 45.833 0.00 0.00 0.00 4.20
2450 2567 6.088137 TCTCTCTCTCTCACATATCTCCCTA 58.912 44.000 0.00 0.00 0.00 3.53
2451 2568 6.013725 TCTCTCTCTCTCACATATCTCCCTAC 60.014 46.154 0.00 0.00 0.00 3.18
2452 2569 5.013704 TCTCTCTCTCACATATCTCCCTACC 59.986 48.000 0.00 0.00 0.00 3.18
2453 2570 4.006989 CTCTCTCACATATCTCCCTACCG 58.993 52.174 0.00 0.00 0.00 4.02
2454 2571 3.394940 TCTCTCACATATCTCCCTACCGT 59.605 47.826 0.00 0.00 0.00 4.83
2455 2572 3.487372 TCTCACATATCTCCCTACCGTG 58.513 50.000 0.00 0.00 0.00 4.94
2456 2573 3.117625 TCTCACATATCTCCCTACCGTGT 60.118 47.826 0.00 0.00 0.00 4.49
2457 2574 3.637229 CTCACATATCTCCCTACCGTGTT 59.363 47.826 0.00 0.00 0.00 3.32
2461 2578 2.249309 ATCTCCCTACCGTGTTCCTT 57.751 50.000 0.00 0.00 0.00 3.36
2511 2638 3.643320 TGATGAGATGCCTATTCTCGGTT 59.357 43.478 0.00 0.00 42.08 4.44
2667 2800 6.250739 CCTTGTGTCGTACGTATCATATATGC 59.749 42.308 16.05 2.06 0.00 3.14
2682 2827 7.792374 TCATATATGCACTCTTTCTCAAACC 57.208 36.000 7.92 0.00 0.00 3.27
2683 2828 6.767902 TCATATATGCACTCTTTCTCAAACCC 59.232 38.462 7.92 0.00 0.00 4.11
2684 2829 1.981256 TGCACTCTTTCTCAAACCCC 58.019 50.000 0.00 0.00 0.00 4.95
2685 2830 1.248486 GCACTCTTTCTCAAACCCCC 58.752 55.000 0.00 0.00 0.00 5.40
2719 2864 2.420129 GGATGTACATGTCCACCTCCAC 60.420 54.545 14.43 2.08 34.57 4.02
2844 3020 5.457140 GCTCCGAATCTAATCTGTAGTGAG 58.543 45.833 0.00 0.00 0.00 3.51
2993 3182 0.951040 AACCGAGGAAAGCAGCGAAG 60.951 55.000 0.00 0.00 0.00 3.79
3036 3225 1.859998 GCTGATTGATTTAACCCGCGC 60.860 52.381 0.00 0.00 0.00 6.86
3037 3226 0.375454 TGATTGATTTAACCCGCGCG 59.625 50.000 25.67 25.67 0.00 6.86
3039 3228 2.640736 ATTGATTTAACCCGCGCGCG 62.641 55.000 43.73 43.73 39.44 6.86
3111 3306 2.357327 CCGATGGCAATGGCAATATG 57.643 50.000 14.81 3.88 42.43 1.78
3112 3307 1.067425 CCGATGGCAATGGCAATATGG 60.067 52.381 14.81 9.38 42.43 2.74
3113 3308 1.670674 CGATGGCAATGGCAATATGGC 60.671 52.381 14.81 14.96 42.43 4.40
3130 3325 2.587194 CATTGGCGCGAGGAGGAG 60.587 66.667 12.10 0.00 0.00 3.69
3131 3326 3.854669 ATTGGCGCGAGGAGGAGG 61.855 66.667 12.10 0.00 0.00 4.30
3136 3331 2.496817 CGCGAGGAGGAGGGAAAG 59.503 66.667 0.00 0.00 0.00 2.62
3137 3332 2.352032 CGCGAGGAGGAGGGAAAGT 61.352 63.158 0.00 0.00 0.00 2.66
3138 3333 1.035932 CGCGAGGAGGAGGGAAAGTA 61.036 60.000 0.00 0.00 0.00 2.24
3140 3335 1.134759 GCGAGGAGGAGGGAAAGTAAC 60.135 57.143 0.00 0.00 0.00 2.50
3141 3336 2.176889 CGAGGAGGAGGGAAAGTAACA 58.823 52.381 0.00 0.00 0.00 2.41
3142 3337 2.565834 CGAGGAGGAGGGAAAGTAACAA 59.434 50.000 0.00 0.00 0.00 2.83
3144 3339 3.583526 GAGGAGGAGGGAAAGTAACAAGT 59.416 47.826 0.00 0.00 0.00 3.16
3145 3340 4.759953 AGGAGGAGGGAAAGTAACAAGTA 58.240 43.478 0.00 0.00 0.00 2.24
3209 3404 1.062002 CTTGGTGCGTTGGCTAATACG 59.938 52.381 0.00 0.00 40.82 3.06
3249 3703 3.376935 CTGGCTGGCTACCCGTGAG 62.377 68.421 2.00 0.00 0.00 3.51
3292 3746 4.457496 ACGCCCTGACCTGCATCG 62.457 66.667 0.00 0.00 0.00 3.84
3342 3797 3.121030 CAGTTTCCAGCTCCGGCG 61.121 66.667 0.00 0.00 44.37 6.46
3343 3798 3.626924 AGTTTCCAGCTCCGGCGT 61.627 61.111 6.01 0.00 44.37 5.68
3344 3799 3.423154 GTTTCCAGCTCCGGCGTG 61.423 66.667 6.01 0.00 44.37 5.34
3438 3911 2.026169 TGTCTATCTGTCTGTCCGTCCT 60.026 50.000 0.00 0.00 0.00 3.85
3452 3925 3.371063 TCCTGACGGACGGCACTC 61.371 66.667 0.00 0.00 33.30 3.51
3591 4108 2.007049 GCCTTGGACGGACACATACAG 61.007 57.143 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 265 6.265577 CAACTAGACTTTGTTTCTGGTTTGG 58.734 40.000 0.00 0.00 40.72 3.28
366 372 2.287915 GTCGAGCACACACAGTTTCATT 59.712 45.455 0.00 0.00 0.00 2.57
643 709 0.032615 TGAGGGTGGTGTGGCTTTTT 60.033 50.000 0.00 0.00 0.00 1.94
857 935 3.227614 ACGGTTGGGCTAAAAATCAGTT 58.772 40.909 0.00 0.00 0.00 3.16
892 970 5.924475 ACTTCCGTCTCAAATTACTTGTG 57.076 39.130 0.00 0.00 36.34 3.33
905 983 9.654663 GCTTTCCATATATTATTACTTCCGTCT 57.345 33.333 0.00 0.00 0.00 4.18
908 986 9.653287 TCTGCTTTCCATATATTATTACTTCCG 57.347 33.333 0.00 0.00 0.00 4.30
916 994 7.604164 CGTGACCTTCTGCTTTCCATATATTAT 59.396 37.037 0.00 0.00 0.00 1.28
917 995 6.929049 CGTGACCTTCTGCTTTCCATATATTA 59.071 38.462 0.00 0.00 0.00 0.98
918 996 5.760253 CGTGACCTTCTGCTTTCCATATATT 59.240 40.000 0.00 0.00 0.00 1.28
960 1038 6.993308 TCGCTCTCCATATCTATATAGTGGTC 59.007 42.308 14.44 5.56 0.00 4.02
994 1072 0.472471 ACACCCAGAAAGGCGAGAAA 59.528 50.000 0.00 0.00 35.39 2.52
1226 1306 5.007682 CGGAAATTGAGAAACTAAGGGGAA 58.992 41.667 0.00 0.00 0.00 3.97
1360 1440 6.573434 GCCCAGAAAGAAAGAAAGAAAGAAA 58.427 36.000 0.00 0.00 0.00 2.52
1361 1441 5.221048 CGCCCAGAAAGAAAGAAAGAAAGAA 60.221 40.000 0.00 0.00 0.00 2.52
1362 1442 4.275936 CGCCCAGAAAGAAAGAAAGAAAGA 59.724 41.667 0.00 0.00 0.00 2.52
1363 1443 4.275936 TCGCCCAGAAAGAAAGAAAGAAAG 59.724 41.667 0.00 0.00 0.00 2.62
1599 1683 3.181452 ACGGAGGAAGTACTAGCTAGAGG 60.181 52.174 27.45 1.98 0.00 3.69
1811 1906 3.941483 GCTTTATGCATGTGTGTAGGAGT 59.059 43.478 10.16 0.00 42.31 3.85
2131 2234 5.304357 TGGTCAGTCCGTATCATATCAACAT 59.696 40.000 0.00 0.00 39.52 2.71
2187 2294 3.879295 AGTGGAAATCGTCATATGGCTTG 59.121 43.478 5.65 0.00 0.00 4.01
2415 2532 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2417 2534 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
2419 2536 4.743057 TGTGAGAGAGAGAGAGAGAGAG 57.257 50.000 0.00 0.00 0.00 3.20
2421 2538 7.002250 AGATATGTGAGAGAGAGAGAGAGAG 57.998 44.000 0.00 0.00 0.00 3.20
2424 2541 5.013079 GGGAGATATGTGAGAGAGAGAGAGA 59.987 48.000 0.00 0.00 0.00 3.10
2425 2542 5.013495 AGGGAGATATGTGAGAGAGAGAGAG 59.987 48.000 0.00 0.00 0.00 3.20
2426 2543 4.913355 AGGGAGATATGTGAGAGAGAGAGA 59.087 45.833 0.00 0.00 0.00 3.10
2427 2544 5.246981 AGGGAGATATGTGAGAGAGAGAG 57.753 47.826 0.00 0.00 0.00 3.20
2428 2545 5.013704 GGTAGGGAGATATGTGAGAGAGAGA 59.986 48.000 0.00 0.00 0.00 3.10
2429 2546 5.253330 GGTAGGGAGATATGTGAGAGAGAG 58.747 50.000 0.00 0.00 0.00 3.20
2430 2547 4.263112 CGGTAGGGAGATATGTGAGAGAGA 60.263 50.000 0.00 0.00 0.00 3.10
2431 2548 4.006989 CGGTAGGGAGATATGTGAGAGAG 58.993 52.174 0.00 0.00 0.00 3.20
2432 2549 3.394940 ACGGTAGGGAGATATGTGAGAGA 59.605 47.826 0.00 0.00 0.00 3.10
2433 2550 3.504134 CACGGTAGGGAGATATGTGAGAG 59.496 52.174 0.00 0.00 0.00 3.20
2434 2551 3.117625 ACACGGTAGGGAGATATGTGAGA 60.118 47.826 0.00 0.00 0.00 3.27
2435 2552 3.223435 ACACGGTAGGGAGATATGTGAG 58.777 50.000 0.00 0.00 0.00 3.51
2436 2553 3.308035 ACACGGTAGGGAGATATGTGA 57.692 47.619 0.00 0.00 0.00 3.58
2437 2554 3.243771 GGAACACGGTAGGGAGATATGTG 60.244 52.174 0.00 0.00 0.00 3.21
2438 2555 2.963782 GGAACACGGTAGGGAGATATGT 59.036 50.000 0.00 0.00 0.00 2.29
2439 2556 3.231818 AGGAACACGGTAGGGAGATATG 58.768 50.000 0.00 0.00 0.00 1.78
2440 2557 3.614568 AGGAACACGGTAGGGAGATAT 57.385 47.619 0.00 0.00 0.00 1.63
2441 2558 3.294214 GAAGGAACACGGTAGGGAGATA 58.706 50.000 0.00 0.00 0.00 1.98
2442 2559 2.108970 GAAGGAACACGGTAGGGAGAT 58.891 52.381 0.00 0.00 0.00 2.75
2443 2560 1.553706 GAAGGAACACGGTAGGGAGA 58.446 55.000 0.00 0.00 0.00 3.71
2444 2561 0.535797 GGAAGGAACACGGTAGGGAG 59.464 60.000 0.00 0.00 0.00 4.30
2445 2562 1.252904 CGGAAGGAACACGGTAGGGA 61.253 60.000 0.00 0.00 0.00 4.20
2446 2563 1.217244 CGGAAGGAACACGGTAGGG 59.783 63.158 0.00 0.00 0.00 3.53
2447 2564 0.389426 CACGGAAGGAACACGGTAGG 60.389 60.000 0.00 0.00 0.00 3.18
2448 2565 0.316204 ACACGGAAGGAACACGGTAG 59.684 55.000 0.00 0.00 0.00 3.18
2449 2566 0.752054 AACACGGAAGGAACACGGTA 59.248 50.000 0.00 0.00 0.00 4.02
2450 2567 0.531311 GAACACGGAAGGAACACGGT 60.531 55.000 0.00 0.00 0.00 4.83
2451 2568 1.554042 CGAACACGGAAGGAACACGG 61.554 60.000 0.00 0.00 0.00 4.94
2452 2569 0.872881 ACGAACACGGAAGGAACACG 60.873 55.000 0.00 0.00 0.00 4.49
2453 2570 0.857287 GACGAACACGGAAGGAACAC 59.143 55.000 0.00 0.00 0.00 3.32
2454 2571 0.748450 AGACGAACACGGAAGGAACA 59.252 50.000 0.00 0.00 0.00 3.18
2455 2572 1.416373 GAGACGAACACGGAAGGAAC 58.584 55.000 0.00 0.00 0.00 3.62
2456 2573 0.316204 GGAGACGAACACGGAAGGAA 59.684 55.000 0.00 0.00 0.00 3.36
2457 2574 1.962144 GGAGACGAACACGGAAGGA 59.038 57.895 0.00 0.00 0.00 3.36
2511 2638 6.878389 TGCATCATGACTAACAACATTACTCA 59.122 34.615 0.00 0.00 0.00 3.41
2608 2738 3.665173 GCTCTTAGCTTCCAAACATCG 57.335 47.619 0.00 0.00 38.45 3.84
2719 2864 3.851458 TGATCTCATCAGGTTCATGGG 57.149 47.619 0.00 0.00 33.59 4.00
2844 3020 3.557595 CCTCCATATTCGTCTGCTTTCAC 59.442 47.826 0.00 0.00 0.00 3.18
3039 3228 2.665185 GCAGGTGTGACGGTGACC 60.665 66.667 0.00 0.00 0.00 4.02
3040 3229 1.301716 ATGCAGGTGTGACGGTGAC 60.302 57.895 0.00 0.00 0.00 3.67
3041 3230 1.301637 CATGCAGGTGTGACGGTGA 60.302 57.895 0.00 0.00 0.00 4.02
3043 3232 2.669569 GCATGCAGGTGTGACGGT 60.670 61.111 14.21 0.00 0.00 4.83
3045 3234 2.191354 CTTGGCATGCAGGTGTGACG 62.191 60.000 21.36 0.00 0.00 4.35
3046 3235 1.582968 CTTGGCATGCAGGTGTGAC 59.417 57.895 21.36 0.00 0.00 3.67
3047 3236 1.604308 CCTTGGCATGCAGGTGTGA 60.604 57.895 21.36 0.00 0.00 3.58
3049 3238 2.993264 GCCTTGGCATGCAGGTGT 60.993 61.111 21.36 0.00 32.06 4.16
3107 3302 1.968017 CCTCGCGCCAATGCCATAT 60.968 57.895 0.00 0.00 0.00 1.78
3108 3303 2.591429 CCTCGCGCCAATGCCATA 60.591 61.111 0.00 0.00 0.00 2.74
3109 3304 4.488136 TCCTCGCGCCAATGCCAT 62.488 61.111 0.00 0.00 0.00 4.40
3112 3307 4.838152 TCCTCCTCGCGCCAATGC 62.838 66.667 0.00 0.00 0.00 3.56
3113 3308 2.587194 CTCCTCCTCGCGCCAATG 60.587 66.667 0.00 0.00 0.00 2.82
3114 3309 3.854669 CCTCCTCCTCGCGCCAAT 61.855 66.667 0.00 0.00 0.00 3.16
3130 3325 3.999001 CCTCCGTTACTTGTTACTTTCCC 59.001 47.826 0.00 0.00 0.00 3.97
3131 3326 4.450080 CACCTCCGTTACTTGTTACTTTCC 59.550 45.833 0.00 0.00 0.00 3.13
3132 3327 4.450080 CCACCTCCGTTACTTGTTACTTTC 59.550 45.833 0.00 0.00 0.00 2.62
3133 3328 4.141642 ACCACCTCCGTTACTTGTTACTTT 60.142 41.667 0.00 0.00 0.00 2.66
3134 3329 3.389002 ACCACCTCCGTTACTTGTTACTT 59.611 43.478 0.00 0.00 0.00 2.24
3136 3331 3.062042 CACCACCTCCGTTACTTGTTAC 58.938 50.000 0.00 0.00 0.00 2.50
3137 3332 2.548493 GCACCACCTCCGTTACTTGTTA 60.548 50.000 0.00 0.00 0.00 2.41
3138 3333 1.812708 GCACCACCTCCGTTACTTGTT 60.813 52.381 0.00 0.00 0.00 2.83
3140 3335 0.953960 GGCACCACCTCCGTTACTTG 60.954 60.000 0.00 0.00 34.51 3.16
3141 3336 1.373812 GGCACCACCTCCGTTACTT 59.626 57.895 0.00 0.00 34.51 2.24
3142 3337 1.198759 ATGGCACCACCTCCGTTACT 61.199 55.000 0.00 0.00 40.22 2.24
3144 3339 1.414919 GATATGGCACCACCTCCGTTA 59.585 52.381 0.00 0.00 40.22 3.18
3145 3340 0.180406 GATATGGCACCACCTCCGTT 59.820 55.000 0.00 0.00 40.22 4.44
3215 3410 1.998222 CCAGCCTAGTAGGAGTACCC 58.002 60.000 21.02 0.61 37.67 3.69
3249 3703 0.320771 AAGCACACCCGTGTCATCTC 60.321 55.000 0.00 0.00 45.50 2.75
3292 3746 0.179018 CAGCTGGGCCTGGTAATACC 60.179 60.000 15.02 1.71 39.22 2.73
3342 3797 1.518133 CTCTGGCTACGCTCTGCAC 60.518 63.158 0.00 0.00 0.00 4.57
3343 3798 1.678970 TCTCTGGCTACGCTCTGCA 60.679 57.895 0.00 0.00 0.00 4.41
3344 3799 1.226831 GTCTCTGGCTACGCTCTGC 60.227 63.158 0.00 0.00 0.00 4.26
3345 3800 1.435515 GGTCTCTGGCTACGCTCTG 59.564 63.158 0.00 0.00 0.00 3.35
3346 3801 2.115911 CGGTCTCTGGCTACGCTCT 61.116 63.158 0.00 0.00 0.00 4.09
3347 3802 2.409651 CGGTCTCTGGCTACGCTC 59.590 66.667 0.00 0.00 0.00 5.03
3348 3803 3.827898 GCGGTCTCTGGCTACGCT 61.828 66.667 0.00 0.00 46.02 5.07
3350 3805 3.127352 GAGGCGGTCTCTGGCTACG 62.127 68.421 1.53 0.00 42.99 3.51
3351 3806 2.787567 GGAGGCGGTCTCTGGCTAC 61.788 68.421 9.80 1.75 42.99 3.58
3352 3807 2.442272 GGAGGCGGTCTCTGGCTA 60.442 66.667 9.80 0.00 42.99 3.93
3465 3938 1.303888 TCTCGTGAGGCGTAAGGGT 60.304 57.895 0.00 0.00 42.13 4.34
3642 4159 3.348236 GTGAGCAACAGCACCCTG 58.652 61.111 0.00 0.00 44.80 4.45


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.